Variant report

Variant	rs17651741
Chromosome Location	chr15:38869666-38869667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:38854764..38859679-chr15:38865029..38869985,6	MCF-7	breast:
2	chr15:38855340..38858194-chr15:38869268..38870820,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11857596	1.00[YRI][hapmap]
rs16967103	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16967104	0.88[EUR][1000 genomes]
rs16967112	0.87[EUR][1000 genomes]
rs16967120	1.00[CHD][hapmap];0.87[TSI][hapmap]
rs17574546	0.87[EUR][1000 genomes]
rs17652674	0.88[EUR][1000 genomes]
rs28438860	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55728265	0.84[AMR][1000 genomes]
rs56059718	0.87[EUR][1000 genomes]
rs56083426	0.92[EUR][1000 genomes]
rs56249992	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60924694	0.87[EUR][1000 genomes]
rs61109886	0.87[EUR][1000 genomes]
rs61573680	0.87[EUR][1000 genomes]
rs7171171	0.87[EUR][1000 genomes]
rs72727394	0.82[EUR][1000 genomes]
rs72729306	0.91[EUR][1000 genomes]
rs72729314	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv904085	chr15:38786114-38985513	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv904086	chr15:38829198-38931396	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17651741	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx
rs17651741	RP11-275I4.2	cis	Esophagus Mucosa	GTEx
rs17651741	C15orf41	cis	cerebellum	SCAN
rs17651741	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL
rs17651741	C15orf54	cis	parietal	SCAN
rs17651741	ARHGAP11A	cis	parietal	SCAN
rs17651741	RASGRP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38865600-38871800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr15:38865600-38881000	Weak transcription	Fetal Thymus	thymus
3	chr15:38866800-38871200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr15:38867000-38871600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:38867400-38872000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr15:38868000-38870800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr15:38868200-38870600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:38868200-38870800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr15:38868400-38870600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr15:38868400-38870800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:38868600-38871000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr15:38868800-38871000	Enhancers	Primary T cells from cord blood	blood
13	chr15:38869000-38869800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:38869000-38870800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr15:38869200-38869800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:38869200-38870200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:38869400-38869800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr15:38869400-38870200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:38869400-38871800	Weak transcription	Thymus	Thymus
20	chr15:38869600-38870400	Enhancers	Brain Germinal Matrix	brain

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